Command & Conquer 3 features returning aspects of gameplay from the previous series. The player oversees the action, ordering multiple units to move and attack targets. The construction yard, a moveable base, is the central platform from which the player constructs other structures. Certain structures can then produce units and resources are needed in order to fund the continuous building of structures and units. Typically the player's primary goal is to defeat an enemy by assaulting and destroying their base, while defending their own.

A supporting structure, a crane, can be constructed which can also construct structures. Thus, when multiple production structures of the same type, such as cranes and barracks, are built, the player is given more queues from which to train and produce units and structures. Though these simultaneously save time, funds are deducted for the extra cost as well; careful management of production, training units and funds are key to strategy. When a structure is built, the player can select anywhere near an existing structure to place it, gaining more territorial control.

Tiberium is the sole resource and is usually gathered from fields of Tiberium crystals scattered around the map. The crystals are gathered by harvester vehicles which unload their cargo into refineries, supplying the player with credits which are then automatically used when training units and building structures. Certain maps also feature Tiberium spikes, which, when captured by the faction's engineer unit, allocate a certain number of funds per second. Other neutral structures, such as an EMP weapon, are also present on maps to be captured. Base defense is provided by specialized defensive towers which are placed within a structure's territory.

All three factions have structures and units with similar functions at their disposal. However, they are adjusted to fit each faction's theme and have somewhat varying properties. Units can be classified into infantry, vehicles and aircraft, each with their own specialities. Unit effectiveness against opponents follows the rock-paper-scissors principle found in most real-time strategy games. Virtually every type of structure in the game acts as a tech tree and additional units, structures and faction-specific abilities will become available to research and create as new structures are built. Production and construction may become temporarily blocked if the required structures are destroyed, or if they are not provided with adequate power by the supporting "power plant" structures. A highly destructive superweapon for each faction can also be constructed and used after a certain timer expires. Once used, the timer must expire again before the superweapon can be activated for an additional time.